Brian
I had faced a similar situation at our institution about a year ago and was succcessfully able to have AC grandfathered in .
Enlist some allies. My guess is that they are others in your area who use the system and are in the same boat and do not want to change to a more cumbersome more expensive system. If the decision makers hear from more than one group it becomes much more difficult to imposr their will. Wendell who posts here frequently was probably the most helpful
Be vocal in asking questions about the decision process and why AC was not included. This was actually quites fun for me as I was able to tell them that AC is CCHIT certified , ranked number one by most all of the independent rankings Medscape.KLAS AAFP ACP etc. . I was able as a solo practioner without any assistance or expense attest to Medicare MU without anyones help faster than the people in their chosen system. I also was able to meet the Aco quality requirements as well and susbsequently did quite well financially as a result.
I think the point to hammer home would be that they are excluding a system that works just as well if not better and that it would cost them more in the long run.
Hope this helps Go get em
Jeff Gindorf MD